jebl.evolution.substmodel
Interface RateMatrix

All Superinterfaces:

Cloneable, Serializable

All Known Implementing Classes:

AbstractRateMatrix, AminoAcidModel, WAG

public interface RateMatrix
extends Cloneable, Serializable

abstract base class for all rate matrices

Author:

Korbinian Strimmer, Alexei Drummond, Matthew Goode

Method Summary

int	getDimension()
double[]	getEquilibriumFrequencies()
double	getEquilibriumFrequency(int i)
double[][]	getRelativeRates()
SequenceType	getSequenceType() Get the data type of this rate matrix
void	getTransitionProbabilities(double[][] probabilityStore) A utility method for speed, transfers trans prob information quickly into store.
double	getTransitionProbability(int fromState, int toState)
String	getUniqueName()
void	setDistance(double distance) Sets the distance (such as time/branch length) used when calculating the probabilities.

Method Detail

getUniqueName

String getUniqueName()

Returns:

a short unique human-readable identifier for this rate matrix.

getDimension

int getDimension()

Returns:

the dimension of this rate matrix.

getEquilibriumFrequencies

double[] getEquilibriumFrequencies()

Returns:

stationary frequencies (sum = 1.0)

getEquilibriumFrequency

double getEquilibriumFrequency(int i)

Returns:

stationary frequency (sum = 1.0) for ith state Preferred method for infrequent use.

getSequenceType

SequenceType getSequenceType()

Get the data type of this rate matrix

getRelativeRates

double[][] getRelativeRates()

Returns:

rate matrix (transition: from 1st index to 2nd index)

getTransitionProbability

double getTransitionProbability(int fromState,
                                int toState)

Parameters:

fromState - The state from which we are starting

toState - The resulting state

Returns:

the probability of going from one state to another given the current distance

getTransitionProbabilities

void getTransitionProbabilities(double[][] probabilityStore)

A utility method for speed, transfers trans prob information quickly into store.

setDistance

void setDistance(double distance)

Sets the distance (such as time/branch length) used when calculating the probabilities. This method may well take the most time!